The '05 Mustang uses a SOHC Cologne motor, so it should work, at least in theory.
I'm not a V-6 guy; most of my knowledge is about the "modular" V-8 motors. The modular motors are notorious for having non-interchangeable parts. The original 4V aluminum mod motors were made in Italy by a subcontractor. Later mod motors were built in Romeo, MI and then Windsor, ON. Mixing parts from the three different plants is near impossible.
AFAIK this is not a problem with the Cologne motor. Obviously you don't want to try using parts from a pushrod Cologne in a SOHC Cologne, but other than that I think that you could physically fit some Mustang parts such as an intake into your ST. Beware things like intakes that have the throttle body on the passenger side in the Mustang, and on the driver's side in the ST! Although it's not impossible to extend the wiring, hoses and other parts, it might be more effort than it's worth.
I honestly don't know if an aftermarket manifold for a Mustang would be worth it in a ST. Factory truck intakes tend to be very free-flowing because trucks are meant to operate at higher engine loads than cars, and because there's more room under the hood to put a "no compromises" intake. In fact, it's not uncommon for Mustang owners to use factory truck intakes, heads and other parts as cheap alternatives to aftermarket hi-po parts.
One thing you might want to try is calling the manufacturer. I've had a lot of success in getting great answers and advice about highly technical (and simple too) matters by just calling the 800 number and explaining my problem. In many cases I get connected to the engineer who designed the part; you can't get better support than that!
Another thing to do is drop a line to Torrie at Unleashed Tuning. If you're changing something that is substantially different than the stock part (like to a manifold that makes power from 4-6 grand, but is weak at low RPM), you will most probably need the ECU reprogrammed for the motor to take advantage of what the part has to offer. Torrie may be able to make a tune for your ST with that aftermarket part sight unseen. But it may be necessary to do a dyno tune, so ask first. If you can get to the place where he does the dyno work, and can afford the dyno time, that's by far the best way to go.
